Synthesis and elaboration of N-methylpyrrolidone as an acetamide fragment substitute in bromodomain inhibition

N-Methylpyrrolidone is a solvent molecule which has been shown to compete with acetyl-lysine-containing peptides for binding to bromodomains. From crystallographic studies, it has also been shown to closely mimic the acetamide binding motif in several bromodomains, but has not yet been directly pursued as a fragment in bromodomain inhibition. In this paper, we report the elaboration of N-methylpyrrolidone as a potential lead in fragment-based drug design. Firstly, N-methylpyrrolidone was functionalised to provide points for chemical elaboration. Then, the moiety was incorporated into analogues of the reported bromodomain inhibitor, Olinone. X-ray crystallography revealed that the modified analogues showed comparable binding affinity and structural mimicry to Olinone in the bromodomain binding site.     

Prediction analysis for microbiome sequencing data

One goal of human microbiome studies is to relate host traits with human microbiome compositions. The analysis of microbial community sequencing data presents great statistical challenges, especially when the samples have different library sizes and the data are overdispersed with many zeros. To address these challenges, we introduce a new statistical framework, called predictive analysis in metagenomics via inverse regression (PAMIR), to analyze microbiome sequencing data. Within this framework, an inverse regression model is developed for overdispersed microbiota counts given the trait, and then a prediction rule is constructed by taking advantage of the dimension‐reduction structure in the model. An efficient Monte Carlo expectation‐maximization algorithm is proposed for maximum likelihood estimation. The method is further generalized to accommodate other types of covariates. We demonstrate the advantages of PAMIR through simulations and two real data examples.     

Revell revisited

The controversy of the Classic versus the Exchange theories for the origin of simple chromatid breaks is outlined.

Using BrdU harlequin sister-chromatid differentiation four Revell ratios can be defined and these have been obtained and tested as a block in V79 hamster cells. The values are quite different from the simple predictions. However, values similar to those observed (taken as a block) can be readily simulated from Revell theory by making the assumption that intra-chromatid events are dominant (0.7:0.3). They can also be obtained from contingency modelling of Classic theory using the same assumption plus the additional constraint that there is no contribution from isolated single lesions (Poisson class 1).

If this latter assumption is correct, then the frequency of breaks involving a colour-jump (ratio III) should not decline to zero as the dose falls. A dose-response experiment shows that it does not, but remains approximately constant at about 12%, even in the unirradiated control.

An added complication arises when we discover for the TB/BB situation, that whilst neither breaks nor gaps show any excess BB involvement (sensitisation), lesions involved in interchanges show at least a 2-fold BB excess.

Clearly, the chromatid discontinuities we are scoring are not behaving as would be expected of a residue of unrejoined primary breaks (Classic theory) and we infer also that they are not ‘simple’.     

Soil Solution Chemistry and Element Fluxes in Three European Heathlands and Their Responses to Warming and Drought

Soil water chemistry and element budgets were studied at three northwestern European Calluna vulgaris heathland sites in Denmark (DK), The Netherlands (NL), and Wales (UK). Responses to experimental nighttime warming and early summer drought were followed during a two-year period. Soil solution chemistry measured below the organic soil layer and below the rooting zone and water fluxes estimated with hydrological models were combined to calculate element budgets. Remarkably high N leaching was observed at the NL heath with 18 and 6.4 kg N ha^–1 year^–1 of NO₃–N and NH₄–N leached from the control plots, respectively, indicating that this site is nitrogen saturated. Increased soil temperature of +0.5°C in the heated plots almost doubled the concentrations and losses of NO₃–N and DON at this site. Temperature also increased mobilization of N in the O horizon at the UK and DK heaths in the first year, but, because of high retention of N in the vegetation or mineral soil, there were no significant effects of warming on seepage water NO₃–N and NH₄–N. Retention of P was high at all three sites. In several cases, drought increased concentrations of elements momentarily, but element fluxes decreased because of a lower flux of water. Seepage water DOC and DON was highly significantly correlated at the UK site where losses of N were low, whereas losses of C and N were uncoupled at the NL site where atmospheric N input was greatest. Based on N budgets, calculations of the net change in the C sink or source strength in response to warming suggest no change or an increase in the C sink strength during these early years.     

How<Emphasis Type="Italic"> Daphnia</Emphasis> copes with excess carbon in its food

Animals that maintain near homeostatic elemental ratios may get rid of excess ingested elements from their food in different ways. C regulation was studied in juveniles of Daphnia magna feeding on two Selenastrum capricornutum cultures contrasting in P content (400 and 80 C:P atomic ratios). Both cultures were labelled with ¹⁴C in order to measure Daphnia ingestion and assimilation rates. No significant difference in ingestion rates was observed between P-low and P-rich food, whereas the net assimilation of ¹⁴C was higher in the treatment with P-rich algae. Some Daphnia were also homogeneously labelled over 5 days on radioactive algae to estimate respiration rates and excretion rates of dissolved organic C (DOC). The respiration rate for Daphnia fed with high C:P algae (38.7% of body C day^-1) was significantly higher than for those feeding on low C:P algae (25.3% of body C day^-1). The DOC excretion rate was also higher when animals were fed on P-low algae (13.4% of body C day^-1) than on P-rich algae (5.7% of body C day^-1) . When corrected for respiratory losses, total assimilation of C did not differ significantly between treatments (around 60% of body C day^-1). Judging from these experiments, D. magna can maintain its stoichiometric balance when feeding on unbalanced diets (high C:P) primarily by disposing of excess dietary C via respiration and excretion of DOC.     

Seasonal changes in the microbial community of a salt marsh, measured by phospholipid fatty acid analysis

Microbial activity within the environment can have distinct geochemicaleffects, and so changes in a microbial community structure can result ingeochemical change. We examined seasonal changes in both the microbialcommunityand the geochemistry of an inter-tidal salt marsh in north-west England tocharacterise biogeochemical processes occurring at this site.Phospholipid fatty acid (PLFA) analysis of sediment samples collected atmonthly intervals was used to measure seasonal changes in microbial biomass andcommunity structure. The PLFA data were analysed using multivariate techniques(Ward's method and the Mahalanobis distance metric), and we show that the useofthe Mahalanobis distance metric improves the statistical analysis by providingdetailed information on the reasons samples cluster together and identifyingthedistinguishing features between the separate clusters. Five clusters of likesamples were defined, showing differences in the community structure over thecourse of a year.At all times, the microbial community was dominated by PLFA associated withaerobic bacteria, but this was most pronounced in summer (August). Theabundanceof branched fatty acids, a measure of the biomass of anaerobes, started toincrease later in the year than did those associated with aerobes and thefungalbiomarker 18:26 showed a brief late-summer peak.The salt marsh remained mildly oxic throughout the year despite the increase inmicrobial respiration, suggested by the large increases in the abundance ofPLFA, in the warmer months. The conditions therefore remained most favourablefor aerobic species throughout the year, explaining their continual dominanceatthis site. However, as the abundance of PLFA synthesised by anaerobesincreased,increases in dissolved Mn concentrations were observed, which we suggest weredue to anaerobic respiration of Mn(IV) to Mn(II). Overall, the geochemicalconditions were consistent with the microbial community structure and changeswithin it.     

Basis of the Relationship between Ash Content in the Flag Leaf and Carbon Isotope Discrimination in Kernels of Durum Wheat

The relationship between ash content and carbon isotope discrimination () was studied in durum wheat (Triticum durum Desf.) grown in a Mediterranean region (Northwest Syria) under three different water regimes (hereafter referred to as environments). In two of these environments, 144 genotypes were cultivated under rain-fed conditions. In the third environment, 125 genotypes were cultivated under irrigation. Ash content was measured in the flag leaf about 3 weeks after anthesis, whereas was analysed in mature kernels. Total transpiration of the photosynthetic tissues of the culm contributing, from heading to maturity, to the filling of kernels was also estimated. Leaf ash content, expressed either on dry matter or leaf area basis or as total ash per blade, correlated positively (p< 0.001) with in the three environments. However, this relationship was not the result of a positive correlation across genotypes between and tissue water content. Moreover, only a small part of the variation in across genotypes was explained by concomitant changes in ash content. When all genotypes across the three environments were plotted, and ash content followed a non-linear relationship (r ² = 74), with tending to a plateau as the ash content increased. However, for the set of genotypes and environments combined, total ash content per leaf blade was positively and linearly related (r ² = 0.76) with the accumulated culm transpiration. The non-linear nature of the relationship between ash content and is sustained by the fact that culm transpiration also showed a non-linear relationship with kernel . Therefore, differences in leaf ash content between environments, and to a lesser extent between genotypes, seem to be brought about by variations in accumulated transpiration during grain formation.